diff --git a/doc/txt/Packages_details.txt b/doc/txt/Packages_details.txt deleted file mode 100644 index fc30c045cf..0000000000 --- a/doc/txt/Packages_details.txt +++ /dev/null @@ -1,2157 +0,0 @@ -"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS -Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -Package details :h3 - -Here is a brief description of all the standard and user packages in -LAMMPS. It lists authors (if applicable) and summarizes the package -contents. It has specific instructions on how to install the package, -including, if necessary, info on how to download or build any extra -library it requires. It also gives links to documentation, example -scripts, and pictures/movies (if available) that illustrate use of the -package. - -The majority of packages can be included in a LAMMPS build with a -single setting (-D PGK_NAME for CMake) or command ("make yes-name" for -make). See the "Build package"_Build_package.html doc page for more -info. A few packages may require additional steps; this is indicated -in the descriptions below. The "Build extras"_Build_extras.html doc -page gives those details. - -NOTE: To see the complete list of commands a package adds to LAMMPS, -you can examine the files in its src directory, e.g. "ls -src/GRANULAR". Files with names that start with fix, compute, atom, -pair, bond, angle, etc correspond to commands with the same style name -as contained in the file name. - -"ASPHERE"_#PKG-ASPHERE, -"BODY"_#PKG-BODY, -"CLASS2"_#PKG-CLASS2, -"COLLOID"_#PKG-COLLOID, -"COMPRESS"_#PKG-COMPRESS, -"CORESHELL"_#PKG-CORESHELL, -"DIPOLE"_#PKG-DIPOLE, -"GPU"_#PKG-GPU, -"GRANULAR"_#PKG-GRANULAR, -"KIM"_#PKG-KIM, -"KOKKOS"_#PKG-KOKKOS, -"KSPACE"_#PKG-KSPACE, -"LATTE"_#PKG-LATTE, -"MANYBODY"_#PKG-MANYBODY, -"MC"_#PKG-MC, -"MESSAGE"_#PKG-MESSAGE, -"MISC"_#PKG-MISC, -"MOLECULE"_#PKG-MOLECULE, -"MPIIO"_#PKG-MPIIO, -"MSCG"_#PKG-MSCG, -"OPT"_#PKG-OPT, -"PERI"_#PKG-PERI, -"POEMS"_#PKG-POEMS, -"PYTHON"_#PKG-PYTHON, -"QEQ"_#PKG-QEQ, -"REPLICA"_#PKG-REPLICA2, -"RIGID"_#PKG-RIGID, -"SHOCK"_#PKG-SHOCK, -"SNAP"_#PKG-SNAP, -"SPIN"_#PKG-SPIN, -"SRD"_#PKG-SRD, -"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c) - -"USER-ADIOS"_#PKG-USER-ADIOS, -"USER-ATC"_#PKG-USER-ATC, -"USER-AWPMD"_#PKG-USER-AWPMD, -"USER-BOCS"_#PKG-USER-BOCS, -"USER-CGDNA"_#PKG-USER-CGDNA, -"USER-CGSDK"_#PKG-USER-CGSDK, -"USER-COLVARS"_#PKG-USER-COLVARS, -"USER-DIFFRACTION"_#PKG-USER-DIFFRACTION, -"USER-DPD"_#PKG-USER-DPD, -"USER-DRUDE"_#PKG-USER-DRUDE, -"USER-EFF"_#PKG-USER-EFF, -"USER-FEP"_#PKG-USER-FEP, -"USER-H5MD"_#PKG-USER-H5MD, -"USER-INTEL"_#PKG-USER-INTEL, -"USER-LB"_#PKG-USER-LB, -"USER-MANIFOLD"_#PKG-USER-MANIFOLD, -"USER-MEAMC"_#PKG-USER-MEAMC, -"USER-MESO"_#PKG-USER-MESO, -"USER-MGPT"_#PKG-USER-MGPT, -"USER-MISC"_#PKG-USER-MISC, -"USER-MOFFF"_#PKG-USER-MOFFF, -"USER-MOLFILE"_#PKG-USER-MOLFILE, -"USER-NETCDF"_#PKG-USER-NETCDF, -"USER-OMP"_#PKG-USER-OMP, -"USER-PHONON"_#PKG-USER-PHONON, -"USER-PLUMED"_#PKG-USER-PLUMED, -"USER-PTM"_#PKG-USER-PTM, -"USER-QMMM"_#PKG-USER-QMMM, -"USER-QTB"_#PKG-USER-QTB, -"USER-QUIP"_#PKG-USER-QUIP, -"USER-REAXC"_#PKG-USER-REAXC, -"USER-SCAFACOS"_#PKG-USER-SCAFACOS, -"USER-SDPD"_#PKG-USER-SDPD, -"USER-SMD"_#PKG-USER-SMD, -"USER-SMTBQ"_#PKG-USER-SMTBQ, -"USER-SPH"_#PKG-USER-SPH, -"USER-TALLY"_#PKG-USER-TALLY, -"USER-UEF"_#PKG-USER-UEF, -"USER-VTK"_#PKG-USER-VTK, -"USER-YAFF"_#PKG-USER-YAFF, :tb(c=6,ea=c) - -:line - -ASPHERE package :link(PKG-ASPHERE),h4 - -[Contents:] - -Computes, time-integration fixes, and pair styles for aspherical -particle models including ellipsoids, 2d lines, and 3d triangles. - -[Supporting info:] - -src/ASPHERE: filenames -> commands -"Howto spherical"_Howto_spherical.html -"pair_style gayberne"_pair_gayberne.html -"pair_style resquared"_pair_resquared.html -"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf -"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf -examples/ASPHERE -examples/ellipse -http://lammps.sandia.gov/movies.html#line -http://lammps.sandia.gov/movies.html#tri :ul - -:line - -BODY package :link(PKG-BODY),h4 - -[Contents:] - -Body-style particles with internal structure. Computes, -time-integration fixes, pair styles, as well as the body styles -themselves. See the "Howto body"_Howto_body.html doc page for an -overview. - -[Supporting info:] - -src/BODY filenames -> commands -"Howto_body"_Howto_body.html -"atom_style body"_atom_style.html -"fix nve/body"_fix_nve_body.html -"pair_style body/nparticle"_pair_body_nparticle.html -examples/body :ul - -:line - -CLASS2 package :link(PKG-CLASS2),h4 - -[Contents:] - -Bond, angle, dihedral, improper, and pair styles for the COMPASS -CLASS2 molecular force field. - -[Supporting info:] - -src/CLASS2: filenames -> commands -"bond_style class2"_bond_class2.html -"angle_style class2"_angle_class2.html -"dihedral_style class2"_dihedral_class2.html -"improper_style class2"_improper_class2.html -"pair_style lj/class2"_pair_class2.html :ul - -:line - -COLLOID package :link(PKG-COLLOID),h4 - -[Contents:] - -Coarse-grained finite-size colloidal particles. Pair styles and fix -wall styles for colloidal interactions. Includes the Fast Lubrication -Dynamics (FLD) method for hydrodynamic interactions, which is a -simplified approximation to Stokesian dynamics. - -[Authors:] This package includes Fast Lubrication Dynamics pair styles -which were created by Amit Kumar and Michael Bybee from Jonathan -Higdon's group at UIUC. - -[Supporting info:] - -src/COLLOID: filenames -> commands -"fix wall/colloid"_fix_wall.html -"pair_style colloid"_pair_colloid.html -"pair_style yukawa/colloid"_pair_yukawa_colloid.html -"pair_style brownian"_pair_brownian.html -"pair_style lubricate"_pair_lubricate.html -"pair_style lubricateU"_pair_lubricateU.html -examples/colloid -examples/srd :ul - -:line - -COMPRESS package :link(PKG-COMPRESS),h4 - -[Contents:] - -Compressed output of dump files via the zlib compression library, -using dump styles with a "gz" in their style name. - -To use this package you must have the zlib compression library -available on your system. - -[Author:] Axel Kohlmeyer (Temple U). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#compress on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/COMPRESS: filenames -> commands -src/COMPRESS/README -lib/compress/README -"dump atom/gz"_dump.html -"dump cfg/gz"_dump.html -"dump custom/gz"_dump.html -"dump xyz/gz"_dump.html :ul - -:line - -CORESHELL package :link(PKG-CORESHELL),h4 - -[Contents:] - -Compute and pair styles that implement the adiabatic core/shell model -for polarizability. The pair styles augment Born, Buckingham, and -Lennard-Jones styles with core/shell capabilities. The "compute -temp/cs"_compute_temp_cs.html command calculates the temperature of a -system with core/shell particles. See the "Howto -coreshell"_Howto_coreshell.html doc page for an overview of how to use -this package. - -[Author:] Hendrik Heenen (Technical U of Munich). - -[Supporting info:] - -src/CORESHELL: filenames -> commands -"Howto coreshell"_Howto_coreshell.html -"Howto polarizable"_Howto_polarizable.html -"compute temp/cs"_compute_temp_cs.html -"pair_style born/coul/long/cs"_pair_cs.html -"pair_style buck/coul/long/cs"_pair_cs.html -"pair_style lj/cut/coul/long/cs"_pair_lj.html -examples/coreshell :ul - -:line - -DIPOLE package :link(PKG-DIPOLE),h4 - -[Contents:] - -An atom style and several pair styles for point dipole models with -short-range or long-range interactions. - -[Supporting info:] - -src/DIPOLE: filenames -> commands -"atom_style dipole"_atom_style.html -"pair_style lj/cut/dipole/cut"_pair_dipole.html -"pair_style lj/cut/dipole/long"_pair_dipole.html -"pair_style lj/long/dipole/long"_pair_dipole.html -examples/dipole :ul - -:line - -GPU package :link(PKG-GPU),h4 - -[Contents:] - -Dozens of pair styles and a version of the PPPM long-range Coulombic -solver optimized for GPUs. All such styles have a "gpu" as a suffix -in their style name. The GPU code can be compiled with either CUDA or -OpenCL, however the OpenCL variants are no longer actively maintained -and only the CUDA versions are regularly tested. The "Speed -gpu"_Speed_gpu.html doc page gives details of what hardware and GPU -software is required on your system, and details on how to build and -use this package. Its styles can be invoked at run time via the "-sf -gpu" or "-suffix gpu" "command-line switches"_Run_options.html. See -also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles. - -[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen -(Northwestern U) while at ORNL. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#gpu on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/GPU: filenames -> commands -src/GPU/README -lib/gpu/README -"Speed packages"_Speed_packages.html -"Speed gpu"_Speed_gpu.html -"Section 2.6 -sf gpu"_Run_options.html -"Section 2.6 -pk gpu"_Run_options.html -"package gpu"_package.html -"Commands all"_lc pages (pair,kspace) for styles followed by (g) -"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul - -:line - -GRANULAR package :link(PKG-GRANULAR),h4 - -[Contents:] - -Pair styles and fixes for finite-size granular particles, which -interact with each other and boundaries via frictional and dissipative -potentials. - -[Supporting info:] - -src/GRANULAR: filenames -> commands -"Howto granular"_Howto_granular.html -"fix pour"_fix_pour.html -"fix wall/gran"_fix_wall_gran.html -"pair_style gran/hooke"_pair_gran.html -"pair_style gran/hertz/history"_pair_gran.html -examples/granregion -examples/pour -bench/in.chute -http://lammps.sandia.gov/pictures.html#jamming -http://lammps.sandia.gov/movies.html#hopper -http://lammps.sandia.gov/movies.html#dem -http://lammps.sandia.gov/movies.html#brazil -http://lammps.sandia.gov/movies.html#granregion :ul - -:line - -KIM package :link(PKG-KIM),h4 - -[Contents:] - -This package contains a set of commands that serve as a wrapper on the -"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org -repository of interatomic models (IMs) -enabling compatible ones to be used in LAMMPS simulations. -This includes "kim_init and kim_interactions"_kim_commands.html -commands to select, initialize and instantiate the IM, and a -"kim_query"_kim_commands.html command to perform web queries -for material property predictions of OpenKIM IMs. -Support for KIM IMs that conform to the -"KIM Application Programming Interface (API)"_https://openkim.org/kim-api/ -is provided by the "pair_style kim"_pair_kim.html command. - -NOTE: The command {pair_style kim} is called by {kim_interactions} and -is not recommended to be directly used in input scripts. - -To use this package you must have the KIM API library available on your -system. The KIM API is available for download on the -"OpenKIM website"_https://openkim.org/kim-api/. -When installing LAMMPS from binary, the kim-api package -is a dependency that is automatically downloaded and installed. - -Information about the KIM project can be found at its website: -"https://openkim.org"_https://openkim.org. -The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota) -and is funded by the "National Science Foundation"_https://www.nsf.gov/. - -[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM -API and the {pair_style kim} command. Axel Kohlmeyer (Temple U) and -Ellad Tadmor (U Minnesota) contributed to the "kim_commands"_kim_commands.html -interface in close collaboration with Ryan Elliott. - - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#kim on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -"kim_commands"_kim_commands.html -"pair_style kim"_pair_kim.html -src/KIM: filenames -> commands -src/KIM/README -lib/kim/README -examples/kim :ul - -:line - -KOKKOS package :link(PKG-KOKKOS),h4 - -[Contents:] - -Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute -styles adapted to compile using the Kokkos library which can convert -them to OpenMP or CUDA code so that they run efficiently on multicore -CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their -style name. The "Speed kokkos"_Speed_kokkos.html doc page gives -details of what hardware and software is required on your system, and -how to build and use this package. Its styles can be invoked at run -time via the "-sf kk" or "-suffix kk" "command-line -switches"_Run_options.html. Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT, -"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which -have styles optimized for CPUs, KNLs, and GPUs. - -You must have a C++11 compatible compiler to use this package. -KOKKOS makes extensive use of advanced C++ features, which can -expose compiler bugs, especially when compiling for maximum -performance at high optimization levels. Please see the file -lib/kokkos/README for a list of compilers and their respective -platforms, that are known to work. - -[Authors:] The KOKKOS package was created primarily by Christian Trott -and Stan Moore (Sandia), with contributions from other folks as well. -It uses the open-source "Kokkos library"_https://github.com/kokkos -which was developed by Carter Edwards, Christian Trott, and others at -Sandia, and which is included in the LAMMPS distribution in -lib/kokkos. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#kokkos on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/KOKKOS: filenames -> commands -src/KOKKOS/README -lib/kokkos/README -"Speed packages"_Speed_packages.html -"Speed kokkos"_Speed_kokkos.html -"Section 2.6 -k on ..."_Run_options.html -"Section 2.6 -sf kk"_Run_options.html -"Section 2.6 -pk kokkos"_Run_options.html -"package kokkos"_package.html -"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k) -"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul - -:line - -KSPACE package :link(PKG-KSPACE),h4 - -[Contents:] - -A variety of long-range Coulombic solvers, as well as pair styles -which compute the corresponding short-range pairwise Coulombic -interactions. These include Ewald, particle-particle particle-mesh -(PPPM), and multilevel summation method (MSM) solvers. - -[Install:] - -Building with this package requires a 1d FFT library be present on -your system for use by the PPPM solvers. This can be the KISS FFT -library provided with LAMMPS, 3rd party libraries like FFTW, or a -vendor-supplied FFT library. See the "Build -settings"_Build_settings.html doc page for details on how to select -different FFT options for your LAMPMS build. - -[Supporting info:] - -src/KSPACE: filenames -> commands -"kspace_style"_kspace_style.html -"doc/PDF/kspace.pdf"_PDF/kspace.pdf -"Howto tip3p"_Howto_tip3p.html -"Howto tip4p"_Howto_tip4p.html -"Howto spc"_Howto_spc.html -"pair_style coul"_pair_coul.html -"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name -examples/peptide -bench/in.rhodo :ul - -:line - -LATTE package :link(PKG-LATTE),h4 - -[Contents:] - -A fix command which wraps the LATTE DFTB code, so that molecular -dynamics can be run with LAMMPS using density-functional tight-binding -quantum forces calculated by LATTE. - -More information on LATTE can be found at this web site: -"https://github.com/lanl/LATTE"_latte-home. A brief technical -description is given with the "fix latte"_fix_latte.html command. - -:link(latte-home,https://github.com/lanl/LATTE) - -[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE -itself is developed at Los Alamos National Laboratory by Marc -Cawkwell, Anders Niklasson, and Christian Negre. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#latte on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/LATTE: filenames -> commands -src/LATTE/README -lib/latte/README -"fix latte"_fix_latte.html -examples/latte -"LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul - -:line - -MANYBODY package :link(PKG-MANYBODY),h4 - -[Contents:] - -A variety of many-body and bond-order potentials. These include -(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials. - -[Supporting info:] - -src/MANYBODY: filenames -> commands -"Commands pair"_Commands_pair.html page -examples/comb -examples/eim -examples/nb3d -examples/shear -examples/streitz -examples/vashishta -bench/in.eam :ul - -:line - -MC package :link(PKG-MC),h4 - -[Contents:] - -Several fixes and a pair style that have Monte Carlo (MC) or MC-like -attributes. These include fixes for creating, breaking, and swapping -bonds, for performing atomic swaps, and performing grand-canonical MC -(GCMC) in conjunction with dynamics. - -[Supporting info:] - -src/MC: filenames -> commands -"fix atom/swap"_fix_atom_swap.html -"fix bond/break"_fix_bond_break.html -"fix bond/create"_fix_bond_create.html -"fix bond/swap"_fix_bond_swap.html -"fix gcmc"_fix_gcmc.html -"pair_style dsmc"_pair_dsmc.html -http://lammps.sandia.gov/movies.html#gcmc :ul - -:line - -MESSAGE package :link(PKG-MESSAGE),h4 - -[Contents:] - -Commands to use LAMMPS as either a client or server and couple it to -another application. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#message on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/MESSAGE: filenames -> commands -lib/message/README -"message"_message.html -"fix client/md"_fix_client_md.html -"server md"_server_md.html -"server mc"_server_mc.html -examples/message :ul - -:line - -MISC package :link(PKG-MISC),h4 - -[Contents:] - -A variety of compute, fix, pair, dump styles with specialized -capabilities that don't align with other packages. Do a directory -listing, "ls src/MISC", to see the list of commands. - -NOTE: the MISC package contains styles that require using the --restrict flag, when compiling with Intel compilers. - -[Supporting info:] - -src/MISC: filenames -> commands -"compute ti"_compute_ti.html -"fix evaporate"_fix_evaporate.html -"fix orient/fcc"_fix_orient.html -"fix ttm"_fix_ttm.html -"fix thermal/conductivity"_fix_thermal_conductivity.html -"fix viscosity"_fix_viscosity.html -examples/KAPPA -examples/VISCOSITY -http://lammps.sandia.gov/pictures.html#ttm -http://lammps.sandia.gov/movies.html#evaporation :ul - -:line - -MOLECULE package :link(PKG-MOLECULE),h4 - -[Contents:] - -A large number of atom, pair, bond, angle, dihedral, improper styles -that are used to model molecular systems with fixed covalent bonds. -The pair styles include the Dreiding (hydrogen-bonding) and CHARMM -force fields, and a TIP4P water model. - -[Supporting info:] - -src/MOLECULE: filenames -> commands -"atom_style"_atom_style.html -"bond_style"_bond_style.html -"angle_style"_angle_style.html -"dihedral_style"_dihedral_style.html -"improper_style"_improper_style.html -"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html -"pair_style lj/charmm/coul/charmm"_pair_charmm.html -"Howto bioFF"_Howto_bioFF.html -examples/cmap -examples/dreiding -examples/micelle, -examples/peptide -bench/in.chain -bench/in.rhodo :ul - -:line - -MPIIO package :link(PKG-MPIIO),h4 - -[Contents:] - -Support for parallel output/input of dump and restart files via the -MPIIO library. It adds "dump styles"_dump.html with a "mpiio" in -their style name. Restart files with an ".mpiio" suffix are also -written and read in parallel. - -[Supporting info:] - -src/MPIIO: filenames -> commands -"dump"_dump.html -"restart"_restart.html -"write_restart"_write_restart.html -"read_restart"_read_restart.html :ul - -:line - -MSCG package :link(PKG-mscg),h4 - -[Contents:] - -A "fix mscg"_fix_mscg.html command which can parameterize a -Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG -library"_mscg-home. - -:link(mscg-home,https://github.com/uchicago-voth/MSCG-release) - -To use this package you must have the MS-CG library available on your -system. - -[Authors:] The fix was written by Lauren Abbott (Sandia). The MS-CG -library was developed by Jacob Wagner in Greg Voth's group at the -University of Chicago. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#mscg on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/MSCG: filenames -> commands -src/MSCG/README -lib/mscg/README -examples/mscg :ul - -:line - -OPT package :link(PKG-OPT),h4 - -[Contents:] - -A handful of pair styles which are optimized for improved CPU -performance on single or multiple cores. These include EAM, LJ, -CHARMM, and Morse potentials. The styles have an "opt" suffix in -their style name. The "Speed opt"_Speed_opt.html doc page gives -details of how to build and use this package. Its styles can be -invoked at run time via the "-sf opt" or "-suffix opt" "command-line -switches"_Run_options.html. See also the "KOKKOS"_#PKG-KOKKOS, -"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which -have styles optimized for CPU performance. - -[Authors:] James Fischer (High Performance Technologies), David Richie, -and Vincent Natoli (Stone Ridge Technolgy). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#opt on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/OPT: filenames -> commands -"Speed packages"_Speed_packages.html -"Speed opt"_Speed_opt.html -"Section 2.6 -sf opt"_Run_options.html -"Commands pair"_Commands_pair.html for styles followed by (t) -"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul - -:line - -PERI package :link(PKG-PERI),h4 - -[Contents:] - -An atom style, several pair styles which implement different -Peridynamics materials models, and several computes which calculate -diagnostics. Peridynamics is a particle-based meshless continuum -model. - -[Authors:] The original package was created by Mike Parks (Sandia). -Additional Peridynamics models were added by Rezwanur Rahman and John -Foster (UTSA). - -[Supporting info:] - -src/PERI: filenames -> commands -"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf -"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf -"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf -"atom_style peri"_atom_style.html -"pair_style peri/*"_pair_peri.html -"compute damage/atom"_compute_damage_atom.html -"compute plasticity/atom"_compute_plasticity_atom.html -examples/peri -http://lammps.sandia.gov/movies.html#peri :ul - -:line - -POEMS package :link(PKG-POEMS),h4 - -[Contents:] - -A fix that wraps the Parallelizable Open source Efficient Multibody -Software (POEMS) library, which is able to simulate the dynamics of -articulated body systems. These are systems with multiple rigid -bodies (collections of particles) whose motion is coupled by -connections at hinge points. - -[Author:] Rudra Mukherjee (JPL) while at RPI. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#poems on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/POEMS: filenames -> commands -src/POEMS/README -lib/poems/README -"fix poems"_fix_poems.html -examples/rigid :ul - -:line - -PYTHON package :link(PKG-PYTHON),h4 - -[Contents:] - -A "python"_python.html command which allow you to execute Python code -from a LAMMPS input script. The code can be in a separate file or -embedded in the input script itself. See the "Python -call"_Python_call.html doc page for an overview of using Python from -LAMMPS in this manner and all the "Python"_Python_head.html doc pages -for other ways to use LAMMPS and Python together. - -NOTE: Building with the PYTHON package assumes you have a Python -shared library available on your system, which needs to be a Python 2 -version, 2.6 or later. Python 3 is not yet supported. See the -lib/python/README for more details. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#python on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/PYTHON: filenames -> commands -"Python call"_Python_head.html -lib/python/README -examples/python :ul - -:line - -QEQ package :link(PKG-QEQ),h4 - -[Contents:] - -Several fixes for performing charge equilibration (QEq) via different -algorithms. These can be used with pair styles that perform QEq as -part of their formulation. - -[Supporting info:] - -src/QEQ: filenames -> commands -"fix qeq/*"_fix_qeq.html -examples/qeq -examples/streitz :ul - -:line - -REPLICA package :link(PKG-REPLICA2),h4 - -[Contents:] - -A collection of multi-replica methods which can be used when running -multiple LAMMPS simulations (replicas). See the "Howto -replica"_Howto_replica.html doc page for an overview of how to run -multi-replica simulations in LAMMPS. Methods in the package include -nudged elastic band (NEB), parallel replica dynamics (PRD), -temperature accelerated dynamics (TAD), parallel tempering, and a -verlet/split algorithm for performing long-range Coulombics on one set -of processors, and the remainder of the force field calculation on -another set. - -[Supporting info:] - -src/REPLICA: filenames -> commands -"Howto replica"_Howto_replica.html -"neb"_neb.html -"prd"_prd.html -"tad"_tad.html -"temper"_temper.html, -"run_style verlet/split"_run_style.html -examples/neb -examples/prd -examples/tad :ul - -:line - -RIGID package :link(PKG-RIGID),h4 - -[Contents:] - -Fixes which enforce rigid constraints on collections of atoms or -particles. This includes SHAKE and RATTLE, as well as various -rigid-body integrators for a few large bodies or many small bodies. -Also several computes which calculate properties of rigid bodies. - -[Supporting info:] - -src/RIGID: filenames -> commands -"compute erotate/rigid"_compute_erotate_rigid.html -fix shake"_fix_shake.html -"fix rattle"_fix_shake.html -"fix rigid/*"_fix_rigid.html -examples/ASPHERE -examples/rigid -bench/in.rhodo -http://lammps.sandia.gov/movies.html#box -http://lammps.sandia.gov/movies.html#star :ul - -:line - -SHOCK package :link(PKG-SHOCK),h4 - -[Contents:] - -Fixes for running impact simulations where a shock-wave passes through -a material. - -[Supporting info:] - -src/SHOCK: filenames -> commands -"fix append/atoms"_fix_append_atoms.html -"fix msst"_fix_msst.html -"fix nphug"_fix_nphug.html -"fix wall/piston"_fix_wall_piston.html -examples/hugoniostat -examples/msst :ul - -:line - -SNAP package :link(PKG-SNAP),h4 - -[Contents:] - -A pair style for the spectral neighbor analysis potential (SNAP). -SNAP is methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. Also several -computes which analyze attributes of the potential. - -[Author:] Aidan Thompson (Sandia). - -[Supporting info:] - -src/SNAP: filenames -> commands -"pair_style snap"_pair_snap.html -"compute sna/atom"_compute_sna_atom.html -"compute snad/atom"_compute_sna_atom.html -"compute snav/atom"_compute_sna_atom.html -examples/snap :ul - -:line - -SPIN package :link(PKG-SPIN),h4 - -[Contents:] - -Model atomic magnetic spins classically, coupled to atoms moving in -the usual manner via MD. Various pair, fix, and compute styles. - -[Author:] Julien Tranchida (Sandia). - -[Supporting info:] - -src/SPIN: filenames -> commands -"Howto spins"_Howto_spins.html -"pair_style spin/dipole/cut"_pair_spin_dipole.html -"pair_style spin/dipole/long"_pair_spin_dipole.html -"pair_style spin/dmi"_pair_spin_dmi.html -"pair_style spin/exchange"_pair_spin_exchange.html -"pair_style spin/magelec"_pair_spin_magelec.html -"pair_style spin/neel"_pair_spin_neel.html -"fix nve/spin"_fix_nve_spin.html -"fix precession/spin"_fix_precession_spin.html -"compute spin"_compute_spin.html -"neb/spin"_neb_spin.html -examples/SPIN :ul - -:line - -SRD package :link(PKG-SRD),h4 - -[Contents:] - -A pair of fixes which implement the Stochastic Rotation Dynamics (SRD) -method for coarse-graining of a solvent, typically around large -colloidal particles. - -[Supporting info:] - -src/SRD: filenames -> commands -"fix srd"_fix_srd.html -"fix wall/srd"_fix_wall_srd.html -examples/srd -examples/ASPHERE -http://lammps.sandia.gov/movies.html#tri -http://lammps.sandia.gov/movies.html#line -http://lammps.sandia.gov/movies.html#poly :ul - -:line - -VORONOI package :link(PKG-VORONOI),h4 - -[Contents:] - -A compute command which calculates the Voronoi tesselation of a -collection of atoms by wrapping the "Voro++ library"_voro-home. This -can be used to calculate the local volume or each atoms or its near -neighbors. - -:link(voro-home,http://math.lbl.gov/voro++) - -To use this package you must have the Voro++ library available on your -system. - -[Author:] Daniel Schwen (INL) while at LANL. The open-source Voro++ -library was written by Chris Rycroft (Harvard U) while at UC Berkeley -and LBNL. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#voronoi on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/VORONOI: filenames -> commands -src/VORONOI/README -lib/voronoi/README -"compute voronoi/atom"_compute_voronoi_atom.html -examples/voronoi :ul - -:line - -USER-ADIOS package :link(PKG-USER-ADIOS),h4 - -[Contents:] - -ADIOS is a high-performance I/O library. This package implements the -dump "atom/adios" and dump "custom/adios" commands to write data using -the ADIOS library. - -[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-adios on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-ADIOS: filenames -> commands -src/USER-ADIOS/README -examples/USER/adios -https://github.com/ornladios/ADIOS2 :ul - -:line - -USER-ATC package :link(PKG-USER-ATC),h4 - -[Contents:] - -ATC stands for atoms-to-continuum. This package implements a "fix -atc"_fix_atc.html command to either couple molecular dynamics with -continuum finite element equations or perform on-the-fly conversion of -atomic information to continuum fields. - -[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-atc on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-ATC: filenames -> commands -src/USER-ATC/README -"fix atc"_fix_atc.html -examples/USER/atc -http://lammps.sandia.gov/pictures.html#atc :ul - -:line - -USER-AWPMD package :link(PKG-USER-AWPMD),h4 - -[Contents:] - -AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This -package implements an atom, pair, and fix style which allows electrons -to be treated as explicit particles in a classical molecular dynamics -model. - -[Author:] Ilya Valuev (JIHT, Russia). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-awpmd on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-AWPMD: filenames -> commands -src/USER-AWPMD/README -"pair_style awpmd/cut"_pair_awpmd.html -examples/USER/awpmd :ul - -:line - -USER-BOCS package :link(PKG-USER-BOCS),h4 - -[Contents:] - -This package provides "fix bocs"_fix_bocs.html, a modified version -of "fix npt"_fix_nh.html which includes the pressure correction to -the barostat as outlined in: - -N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that -accurately describe the structure, pressure, and compressibility of -molecular liquids," J. Chem. Phys. 143, 243148 (2015). - -[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The -Pennsylvania State University) - -[Supporting info:] - -The USER-BOCS user package for LAMMPS is part of the BOCS software package: -"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS - -See the following reference for information about the entire package: - -Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. -"BOCS: Bottom-Up Open-Source Coarse-Graining Software." -J. Phys. Chem. B. 122, 13, 3363-3377 (2018). - -Example inputs are in the examples/USER/bocs folder. - -:line - -USER-CGDNA package :link(PKG-USER-CGDNA),h4 - -[Contents:] - -Several pair styles, a bond style, and integration fixes for -coarse-grained models of single- and double-stranded DNA based on the -oxDNA model of Doye, Louis and Ouldridge at the University of Oxford. -This includes Langevin-type rigid-body integrators with improved -stability. - -[Author:] Oliver Henrich (University of Strathclyde, Glasgow). - -[Supporting info:] - -src/USER-CGDNA: filenames -> commands -/src/USER-CGDNA/README -"pair_style oxdna/*"_pair_oxdna.html -"pair_style oxdna2/*"_pair_oxdna2.html -"bond_style oxdna/*"_bond_oxdna.html -"bond_style oxdna2/*"_bond_oxdna.html -"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul - -:line - -USER-CGSDK package :link(PKG-USER-CGSDK),h4 - -[Contents:] - -Several pair styles and an angle style which implement the -coarse-grained SDK model of Shinoda, DeVane, and Klein which enables -simulation of ionic liquids, electrolytes, lipids and charged amino -acids. - -[Author:] Axel Kohlmeyer (Temple U). - -[Supporting info:] - -src/USER-CGSDK: filenames -> commands -src/USER-CGSDK/README -"pair_style lj/sdk/*"_pair_sdk.html -"angle_style sdk"_angle_sdk.html -examples/USER/cgsdk -http://lammps.sandia.gov/pictures.html#cg :ul - -:line - -USER-COLVARS package :link(PKG-USER-COLVARS),h4 - -[Contents:] - -COLVARS stands for collective variables, which can be used to -implement various enhanced sampling methods, including Adaptive -Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and -Restraints. A "fix colvars"_fix_colvars.html command is implemented -which wraps a COLVARS library, which implements these methods. -simulations. - -[Authors:] The COLVARS library is written and maintained by -Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) -and Jerome Henin (LISM, CNRS, Marseille, France), originally for -the NAMD MD code, but with portability in mind. Axel Kohlmeyer -(Temple U) provided the interface to LAMMPS. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-colvars on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-COLVARS: filenames -> commands -"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf -src/USER-COLVARS/README -lib/colvars/README -"fix colvars"_fix_colvars.html -examples/USER/colvars :ul - -:line - -USER-PLUMED package :link(PKG-USER-PLUMED),h4 - -[Contents:] - -The fix plumed command allows you to use the PLUMED free energy plugin -for molecular dynamics to analyze and bias your LAMMPS trajectory on -the fly. The PLUMED library is called from within the LAMMPS input -script by using the "fix plumed"_fix_plumed.html command. - -[Authors:] The "PLUMED library"_#PLUMED is written and maintained by -Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth -Tribello. - -:link(PLUMED,http://www.plumed.org) - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-plumed on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-PLUMED/README -lib/plumed/README -"fix plumed"_fix_plumed.html -examples/USER/plumed :ul - -:line - -USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4 - -[Contents:] - -Two computes and a fix for calculating x-ray and electron diffraction -intensities based on kinematic diffraction theory. - -[Author:] Shawn Coleman while at the U Arkansas. - -[Supporting info:] - -src/USER-DIFFRACTION: filenames -> commands -"compute saed"_compute_saed.html -"compute xrd"_compute_xrd.html -"fix saed/vtk"_fix_saed_vtk.html -examples/USER/diffraction :ul - -:line - -USER-DPD package :link(PKG-USER-DPD),h4 - -[Contents:] - -DPD stands for dissipative particle dynamics. This package implements -coarse-grained DPD-based models for energetic, reactive molecular -crystalline materials. It includes many pair styles specific to these -systems, including for reactive DPD, where each particle has internal -state for multiple species and a coupled set of chemical reaction ODEs -are integrated each timestep. Highly accurate time integrators for -isothermal, isoenergetic, isobaric and isenthalpic conditions are -included. These enable long timesteps via the Shardlow splitting -algorithm. - -[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John -Brennan (ARL). - -[Supporting info:] - -src/USER-DPD: filenames -> commands -/src/USER-DPD/README -"compute dpd"_compute_dpd.html -"compute dpd/atom"_compute_dpd_atom.html -"fix eos/cv"_fix_eos_table.html -"fix eos/table"_fix_eos_table.html -"fix eos/table/rx"_fix_eos_table_rx.html -"fix shardlow"_fix_shardlow.html -"fix rx"_fix_rx.html -"pair_style table/rx"_pair_table_rx.html -"pair_style dpd/fdt"_pair_dpd_fdt.html -"pair_style dpd/fdt/energy"_pair_dpd_fdt.html -"pair_style exp6/rx"_pair_exp6_rx.html -"pair_style multi/lucy"_pair_multi_lucy.html -"pair_style multi/lucy/rx"_pair_multi_lucy_rx.html -examples/USER/dpd :ul - -:line - -USER-DRUDE package :link(PKG-USER-DRUDE),h4 - -[Contents:] - -Fixes, pair styles, and a compute to simulate thermalized Drude -oscillators as a model of polarization. See the "Howto -drude"_Howto_drude.html and "Howto drude2"_Howto_drude2.html doc pages -for an overview of how to use the package. There are auxiliary tools -for using this package in tools/drude. - -[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien -Devemy (CNRS), and Agilio Padua (U Blaise Pascal). - -[Supporting info:] - -src/USER-DRUDE: filenames -> commands -"Howto drude"_Howto_drude.html -"Howto drude2"_Howto_drude2.html -"Howto polarizable"_Howto_polarizable.html -src/USER-DRUDE/README -"fix drude"_fix_drude.html -"fix drude/transform/*"_fix_drude_transform.html -"compute temp/drude"_compute_temp_drude.html -"pair_style thole"_pair_thole.html -"pair_style lj/cut/thole/long"_pair_thole.html -examples/USER/drude -tools/drude :ul - -:line - -USER-EFF package :link(PKG-USER-EFF),h4 - -[Contents:] - -EFF stands for electron force field which allows a classical MD code -to model electrons as particles of variable radius. This package -contains atom, pair, fix and compute styles which implement the eFF as -described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, -JCC, 2010. The eFF potential was first introduced by Su and Goddard, -in 2007. There are auxiliary tools for using this package in -tools/eff; see its README file. - -[Author:] Andres Jaramillo-Botero (CalTech). - -[Supporting info:] - -src/USER-EFF: filenames -> commands -src/USER-EFF/README -"atom_style electron"_atom_style.html -"fix nve/eff"_fix_nve_eff.html -"fix nvt/eff"_fix_nh_eff.html -"fix npt/eff"_fix_nh_eff.html -"fix langevin/eff"_fix_langevin_eff.html -"compute temp/eff"_compute_temp_eff.html -"pair_style eff/cut"_pair_eff.html -"pair_style eff/inline"_pair_eff.html -examples/USER/eff -tools/eff/README -tools/eff -http://lammps.sandia.gov/movies.html#eff :ul - -:line - -USER-FEP package :link(PKG-USER-FEP),h4 - -[Contents:] - -FEP stands for free energy perturbation. This package provides -methods for performing FEP simulations by using a "fix -adapt/fep"_fix_adapt_fep.html command with soft-core pair potentials, -which have a "soft" in their style name. There are auxiliary tools -for using this package in tools/fep; see its README file. - -[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand) - -[Supporting info:] - -src/USER-FEP: filenames -> commands -src/USER-FEP/README -"fix adapt/fep"_fix_adapt_fep.html -"compute fep"_compute_fep.html -"pair_style */soft"_pair_fep_soft.html -examples/USER/fep -tools/fep/README -tools/fep :ul - -:line - -USER-H5MD package :link(PKG-USER-H5MD),h4 - -[Contents:] - -H5MD stands for HDF5 for MD. "HDF5"_HDF5 is a portable, binary, -self-describing file format, used by many scientific simulations. -H5MD is a format for molecular simulations, built on top of HDF5. -This package implements a "dump h5md"_dump_h5md.html command to output -LAMMPS snapshots in this format. - -:link(HDF5,http://www.hdfgroup.org/HDF5) - -To use this package you must have the HDF5 library available on your -system. - -[Author:] Pierre de Buyl (KU Leuven) created both the package and the -H5MD format. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-h5md on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-H5MD: filenames -> commands -src/USER-H5MD/README -lib/h5md/README -"dump h5md"_dump_h5md.html :ul - -:line - -USER-INTEL package :link(PKG-USER-INTEL),h4 - -[Contents:] - -Dozens of pair, fix, bond, angle, dihedral, improper, and kspace -styles which are optimized for Intel CPUs and KNLs (Knights Landing). -All of them have an "intel" in their style name. The "Speed -intel"_Speed_intel.html doc page gives details of what hardware and -compilers are required on your system, and how to build and use this -package. Its styles can be invoked at run time via the "-sf intel" or -"-suffix intel" "command-line switches"_Run_options.html. Also see -the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-OMP"_#PKG-USER-OMP packages, -which have styles optimized for CPUs and KNLs. - -You need to have an Intel compiler, version 14 or higher to take full -advantage of this package. While compilation with GNU compilers is -supported, performance will be sub-optimal. - -NOTE: the USER-INTEL package contains styles that require using the --restrict flag, when compiling with Intel compilers. - -[Author:] Mike Brown (Intel). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-intel on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-INTEL: filenames -> commands -src/USER-INTEL/README -"Speed packages"_Speed_packages.html -"Speed intel"_Speed_intel.html -"Section 2.6 -sf intel"_Run_options.html -"Section 2.6 -pk intel"_Run_options.html -"package intel"_package.html -"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i) -src/USER-INTEL/TEST -"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul - -:line - -USER-LB package :link(PKG-USER-LB),h4 - -[Contents:] - -Fixes which implement a background Lattice-Boltzmann (LB) fluid, which -can be used to model MD particles influenced by hydrodynamic forces. - -[Authors:] Frances Mackay and Colin Denniston (University of Western -Ontario). - -[Supporting info:] - -src/USER-LB: filenames -> commands -src/USER-LB/README -"fix lb/fluid"_fix_lb_fluid.html -"fix lb/momentum"_fix_lb_momentum.html -"fix lb/viscous"_fix_lb_viscous.html -examples/USER/lb :ul - -:line - -USER-MGPT package :link(PKG-USER-MGPT),h4 - -[Contents:] - -A pair style which provides a fast implementation of the quantum-based -MGPT multi-ion potentials. The MGPT or model GPT method derives from -first-principles DFT-based generalized pseudopotential theory (GPT) -through a series of systematic approximations valid for mid-period -transition metals with nearly half-filled d bands. The MGPT method -was originally developed by John Moriarty at LLNL. The pair style in -this package calculates forces and energies using an optimized -matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. - -[Authors:] Tomas Oppelstrup and John Moriarty (LLNL). - -[Supporting info:] - -src/USER-MGPT: filenames -> commands -src/USER-MGPT/README -"pair_style mgpt"_pair_mgpt.html -examples/USER/mgpt :ul - -:line - -USER-MISC package :link(PKG-USER-MISC),h4 - -[Contents:] - -A potpourri of (mostly) unrelated features contributed to LAMMPS by -users. Each feature is a single fix, compute, pair, bond, angle, -dihedral, improper, or command style. - -[Authors:] The author for each style in the package is listed in the -src/USER-MISC/README file. - -[Supporting info:] - -src/USER-MISC: filenames -> commands -src/USER-MISC/README -one doc page per individual command listed in src/USER-MISC/README -examples/USER/misc :ul - -:line - -USER-MANIFOLD package :link(PKG-USER-MANIFOLD),h4 - -[Contents:] - -Several fixes and a "manifold" class which enable simulations of -particles constrained to a manifold (a 2D surface within the 3D -simulation box). This is done by applying the RATTLE constraint -algorithm to formulate single-particle constraint functions -g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) -n = grad(g). - -[Author:] Stefan Paquay (until 2017: Eindhoven University of -Technology (TU/e), The Netherlands; since 2017: Brandeis University, -Waltham, MA, USA) - -[Supporting info:] - -src/USER-MANIFOLD: filenames -> commands -src/USER-MANIFOLD/README -"Howto manifold"_Howto_manifold.html -"fix manifoldforce"_fix_manifoldforce.html -"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html -"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -examples/USER/manifold -http://lammps.sandia.gov/movies.html#manifold :ul - -:line - -USER-MEAMC package :link(PKG-USER-MEAMC),h4 - -[Contents:] - -A pair style for the modified embedded atom (MEAM) potential -translated from the Fortran version in the (obsolete) "MEAM" package -to plain C++. The USER-MEAMC fully replaces the MEAM package, which -has been removed from LAMMPS after the 12 December 2018 version. - -[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg) -based on the Fortran version of Greg Wagner (Northwestern U) while at -Sandia. - -[Supporting info:] - -src/USER-MEAMC: filenames -> commands -src/USER-MEAMC/README -"pair_style meam/c"_pair_meamc.html -examples/meamc :ul - -:line - -USER-MESO package :link(PKG-USER-MESO),h4 - -[Contents:] - -Several extensions of the dissipative particle dynamics (DPD) -method. Specifically, energy-conserving DPD (eDPD) that can model -non-isothermal processes, many-body DPD (mDPD) for simulating -vapor-liquid coexistence, and transport DPD (tDPD) for modeling -advection-diffusion-reaction systems. The equations of motion of these -DPD extensions are integrated through a modified velocity-Verlet (MVV) -algorithm. - -[Author:] Zhen Li (Division of Applied Mathematics, Brown University) - -[Supporting info:] - -src/USER-MESO: filenames -> commands -src/USER-MESO/README -"atom_style edpd"_atom_style.html -"pair_style edpd"_pair_meso.html -"pair_style mdpd"_pair_meso.html -"pair_style tdpd"_pair_meso.html -"fix mvv/dpd"_fix_mvv_dpd.html -examples/USER/meso -http://lammps.sandia.gov/movies.html#mesodpd :ul - -:line - -USER-MOFFF package :link(PKG-USER-MOFFF),h4 - -[Contents:] - -Pair, angle and improper styles needed to employ the MOF-FF -force field by Schmid and coworkers with LAMMPS. -MOF-FF is a first principles derived force field with the primary aim -to simulate MOFs and related porous framework materials, using spherical -Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B -2013, 250, 1128-1141. -For the usage of MOF-FF see the example in the example directory as -well as the "MOF+"_MOFplus website. - -:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF) - -[Author:] Hendrik Heenen (Technical U of Munich), -Rochus Schmid (Ruhr-University Bochum). - -[Supporting info:] - -src/USER-MOFFF: filenames -> commands -src/USER-MOFFF/README -"pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html -"angle_style class2"_angle_class2.html -"angle_style cosine/buck6d"_angle_cosine_buck6d.html -"improper_style inversion/harmonic"_improper_inversion_harmonic.html -examples/USER/mofff :ul - -:line - -USER-MOLFILE package :link(PKG-USER-MOLFILE),h4 - -[Contents:] - -A "dump molfile"_dump_molfile.html command which uses molfile plugins -that are bundled with the "VMD"_vmd-home -molecular visualization and analysis program, to enable LAMMPS to dump -snapshots in formats compatible with various molecular simulation -tools. - -To use this package you must have the desired VMD plugins available on -your system. - -Note that this package only provides the interface code, not the -plugins themselves, which will be accessed when requesting a specific -plugin via the "dump molfile"_dump_molfile.html command. Plugins can -be obtained from a VMD installation which has to match the platform -that you are using to compile LAMMPS for. By adding plugins to VMD, -support for new file formats can be added to LAMMPS (or VMD or other -programs that use them) without having to re-compile the application -itself. More information about the VMD molfile plugins can be found -at -"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile. - -[Author:] Axel Kohlmeyer (Temple U). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-molfile on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-MOLFILE: filenames -> commands -src/USER-MOLFILE/README -lib/molfile/README -"dump molfile"_dump_molfile.html :ul - -:line - -USER-NETCDF package :link(PKG-USER-NETCDF),h4 - -[Contents:] - -Dump styles for writing NetCDF formatted dump files. NetCDF is a -portable, binary, self-describing file format developed on top of -HDF5. The file contents follow the AMBER NetCDF trajectory conventions -(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions. - -To use this package you must have the NetCDF library available on your -system. - -Note that NetCDF files can be directly visualized with the following -tools: - -"Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above) -"VMD"_vmd-home -"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul - -:link(ovito,http://www.ovito.org) -:link(vmd-home,https://www.ks.uiuc.edu/Research/vmd/) -:link(atomeye,http://www.libatoms.org) - -[Author:] Lars Pastewka (Karlsruhe Institute of Technology). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-netcdf on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-NETCDF: filenames -> commands -src/USER-NETCDF/README -lib/netcdf/README -"dump netcdf"_dump_netcdf.html :ul - -:line - -USER-OMP package :link(PKG-USER-OMP),h4 - -[Contents:] - -Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and -kspace styles which are altered to enable threading on many-core CPUs -via OpenMP directives. All of them have an "omp" in their style name. -The "Speed omp"_Speed_omp.html doc page gives details of what hardware -and compilers are required on your system, and how to build and use -this package. Its styles can be invoked at run time via the "-sf omp" -or "-suffix omp" "command-line switches"_Run_options.html. Also see -the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-INTEL"_#PKG-USER-INTEL -packages, which have styles optimized for CPUs. - -[Author:] Axel Kohlmeyer (Temple U). - -NOTE: To enable multi-threading support the compile flag "-fopenmp" -and the link flag "-fopenmp" (for GNU compilers, you have to look up -the equivalent flags for other compilers) must be used to build LAMMPS. -When using Intel compilers, also the "-restrict" flag is required. -The USER-OMP package can be compiled without enabling OpenMP; then -all code will be compiled as serial and the only improvement over the -regular styles are some data access optimization. These flags should -be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine. -See src/MAKE/OPTIONS/Makefile.omp for an example. - -Once you have an appropriate Makefile.machine, you can -install/un-install the package and build LAMMPS in the usual manner: - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-omp on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-OMP: filenames -> commands -src/USER-OMP/README -"Speed packages"_Speed_packages.html -"Speed omp"_Speed_omp.html -"Section 2.6 -sf omp"_Run_options.html -"Section 2.6 -pk omp"_Run_options.html -"package omp"_package.html -"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o) -"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul - -:line - -USER-PHONON package :link(PKG-USER-PHONON),h4 - -[Contents:] - -A "fix phonon"_fix_phonon.html command that calculates dynamical -matrices, which can then be used to compute phonon dispersion -relations, directly from molecular dynamics simulations. -And a "dynamical_matrix"_dynamical_matrix.html as well as a -"third_order"_third_order.html command to compute the dynamical matrix -and third order tensor from finite differences. - -[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" -and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" - - -[Supporting info:] - -src/USER-PHONON: filenames -> commands -src/USER-PHONON/README -"fix phonon"_fix_phonon.html -"dynamical_matrix"_dynamical_matrix.html -"third_order"_third_order.html -examples/USER/phonon :ul - -:line - -USER-PTM package :link(PKG-USER-PTM),h4 - -[Contents:] - -A "compute ptm/atom"_compute_ptm_atom.html command that calculates -local structure characterization using the Polyhedral Template -Matching methodology. - -[Author:] Peter Mahler Larsen (MIT). - -[Supporting info:] - -src/USER-PTM: filenames not starting with ptm_ -> commands -src/USER-PTM: filenames starting with ptm_ -> supporting code -src/USER-PTM/LICENSE -"compute ptm/atom"_compute_ptm_atom.html :ul - -:line - -USER-QMMM package :link(PKG-USER-QMMM),h4 - -[Contents:] - -A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a -QM/MM simulation, currently only in combination with the "Quantum -ESPRESSO"_espresso package. - -:link(espresso,http://www.quantum-espresso.org) - -To use this package you must have Quantum ESPRESSO available on your -system. - -The current implementation only supports an ONIOM style mechanical -coupling to the Quantum ESPRESSO plane wave DFT package. -Electrostatic coupling is in preparation and the interface has been -written in a manner that coupling to other QM codes should be possible -without changes to LAMMPS itself. - -[Author:] Axel Kohlmeyer (Temple U). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-qmmm on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-QMMM: filenames -> commands -src/USER-QMMM/README -lib/qmmm/README -"fix phonon"_fix_phonon.html -lib/qmmm/example-ec/README -lib/qmmm/example-mc/README :ul - -:line - -USER-QTB package :link(PKG-USER-QTB),h4 - -[Contents:] - -Two fixes which provide a self-consistent quantum treatment of -vibrational modes in a classical molecular dynamics simulation. By -coupling the MD simulation to a colored thermostat, it introduces zero -point energy into the system, altering the energy power spectrum and -the heat capacity to account for their quantum nature. This is useful -when modeling systems at temperatures lower than their classical -limits or when temperatures ramp across the classical limits in a -simulation. - -[Author:] Yuan Shen (Stanford U). - -[Supporting info:] - -src/USER-QTB: filenames -> commands -src/USER-QTB/README -"fix qtb"_fix_qtb.html -"fix qbmsst"_fix_qbmsst.html -examples/USER/qtb :ul - -:line - -USER-QUIP package :link(PKG-USER-QUIP),h4 - -[Contents:] - -A "pair_style quip"_pair_quip.html command which wraps the "QUIP -libAtoms library"_quip, which includes a variety of interatomic -potentials, including Gaussian Approximation Potential (GAP) models -developed by the Cambridge University group. - -:link(quip,https://github.com/libAtoms/QUIP) - -To use this package you must have the QUIP libAtoms library available -on your system. - -[Author:] Albert Bartok (Cambridge University) - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-quip on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-QUIP: filenames -> commands -src/USER-QUIP/README -"pair_style quip"_pair_quip.html -examples/USER/quip :ul - -:line - -USER-REAXC package :link(PKG-USER-REAXC),h4 - -[Contents:] - -A pair style which implements the ReaxFF potential in C/C++. ReaxFF -is a universal reactive force field. See the src/USER-REAXC/README file -for more info on differences between the two packages. Also two fixes -for monitoring molecules as bonds are created and destroyed. - -[Author:] Hasan Metin Aktulga (MSU) while at Purdue University. - -[Supporting info:] - -src/USER-REAXC: filenames -> commands -src/USER-REAXC/README -"pair_style reax/c"_pair_reaxc.html -"fix reax/c/bonds"_fix_reaxc_bonds.html -"fix reax/c/species"_fix_reaxc_species.html -examples/reax :ul - -:line - -USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4 - -[Contents:] - -A KSpace style which wraps the "ScaFaCoS Coulomb solver -library"_http://www.scafacos.de to compute long-range Coulombic -interactions. - -To use this package you must have the ScaFaCoS library available on -your system. - -[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command. - -ScaFaCoS itself was developed by a consortium of German research -facilities with a BMBF (German Ministry of Science and Education) -funded project in 2009-2012. Participants of the consortium were the -Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as -the Forschungszentrum Juelich. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-scafacos on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-SCAFACOS: filenames -> commands -src/USER-SCAFACOS/README -"kspace_style scafacos"_kspace_style.html -"kspace_modify"_kspace_modify.html -examples/USER/scafacos :ul - -:line - -USER-SDPD package :link(PKG-USER-SDPD),h4 - -[Contents:] - -A pair style for smoothed dissipative particle dynamics (SDPD), which -is an extension of smoothed particle hydrodynamics (SPH) to mesoscale -where thermal fluctuations are important (see the -"USER-SPH package"_#PKG-USER-SPH). -Also two fixes for moving and rigid body integration of SPH/SDPD particles -(particles of atom_style meso). - -[Author:] Morteza Jalalvand (Institute for Advanced Studies in Basic -Sciences, Iran). - -[Supporting info:] - -src/USER-SDPD: filenames -> commands -src/USER-SDPD/README -"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html -"fix meso/move"_fix_meso_move.html -"fix rigid/meso"_fix_rigid_meso.html -examples/USER/sdpd :ul - -:line - -USER-SMD package :link(PKG-USER-SMD),h4 - -[Contents:] - -An atom style, fixes, computes, and several pair styles which -implements smoothed Mach dynamics (SMD) for solids, which is a model -related to smoothed particle hydrodynamics (SPH) for liquids (see the -"USER-SPH package"_#PKG-USER-SPH). - -This package solves solids mechanics problems via a state of the art -stabilized meshless method with hourglass control. It can specify -hydrostatic interactions independently from material strength models, -i.e. pressure and deviatoric stresses are separated. It provides many -material models (Johnson-Cook, plasticity with hardening, -Mie-Grueneisen, Polynomial EOS) and allows new material models to be -added. It implements rigid boundary conditions (walls) which can be -specified as surface geometries from *.STL files. - -[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed -Dynamics, Ernst Mach Institute, Germany). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-smd on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-SMD: filenames -> commands -src/USER-SMD/README -doc/PDF/SMD_LAMMPS_userguide.pdf -examples/USER/smd -http://lammps.sandia.gov/movies.html#smd :ul - -:line - -USER-SMTBQ package :link(PKG-USER-SMTBQ),h4 - -[Contents:] - -A pair style which implements a Second Moment Tight Binding model with -QEq charge equilibration (SMTBQ) potential for the description of -ionocovalent bonds in oxides. - -[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert -Tetot (LAAS-CNRS, France). - -[Supporting info:] - -src/USER-SMTBQ: filenames -> commands -src/USER-SMTBQ/README -"pair_style smtbq"_pair_smtbq.html -examples/USER/smtbq :ul - -:line - -USER-SPH package :link(PKG-USER-SPH),h4 - -[Contents:] - -An atom style, fixes, computes, and several pair styles which -implements smoothed particle hydrodynamics (SPH) for liquids. See the -related "USER-SMD package"_#PKG-USER-SMD package for smooth Mach dynamics -(SMD) for solids. - -This package contains ideal gas, Lennard-Jones equation of states, -Tait, and full support for complete (i.e. internal-energy dependent) -equations of state. It allows for plain or Monaghans XSPH integration -of the equations of motion. It has options for density continuity or -density summation to propagate the density field. It has -"set"_set.html command options to set the internal energy and density -of particles from the input script and allows the same quantities to -be output with thermodynamic output or to dump files via the "compute -property/atom"_compute_property_atom.html command. - -[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed -Dynamics, Ernst Mach Institute, Germany). - -[Supporting info:] - -src/USER-SPH: filenames -> commands -src/USER-SPH/README -doc/PDF/SPH_LAMMPS_userguide.pdf -examples/USER/sph -http://lammps.sandia.gov/movies.html#sph :ul - -:line - -USER-TALLY package :link(PKG-USER-TALLY),h4 - -[Contents:] - -Several compute styles that can be called when pairwise interactions -are calculated to tally information (forces, heat flux, energy, -stress, etc) about individual interactions. - -[Author:] Axel Kohlmeyer (Temple U). - -[Supporting info:] - -src/USER-TALLY: filenames -> commands -src/USER-TALLY/README -"compute */tally"_compute_tally.html -examples/USER/tally :ul - -:line - -USER-UEF package :link(PKG-USER-UEF),h4 - -[Contents:] - -A fix style for the integration of the equations of motion under -extensional flow with proper boundary conditions, as well as several -supporting compute styles and an output option. - -[Author:] David Nicholson (MIT). - -[Supporting info:] - -src/USER-UEF: filenames -> commands -src/USER-UEF/README -"fix nvt/uef"_fix_nh_uef.html -"fix npt/uef"_fix_nh_uef.html -"compute pressure/uef"_compute_pressure_uef.html -"compute temp/uef"_compute_temp_uef.html -"dump cfg/uef"_dump_cfg_uef.html -examples/uef :ul - -:line - -USER-VTK package :link(PKG-USER-VTK),h4 - -[Contents:] - -A "dump vtk"_dump_vtk.html command which outputs snapshot info in the -"VTK format"_vtk, enabling visualization by "Paraview"_paraview or -other visualization packages. - -:link(vtk,http://www.vtk.org) -:link(paraview,http://www.paraview.org) - -To use this package you must have VTK library available on your -system. - -[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#user-vtk on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/USER-VTK: filenames -> commands -src/USER-VTK/README -lib/vtk/README -"dump vtk"_dump_vtk.html :ul - - -:line - -USER-YAFF package :link(PKG-USER-YAFF),h4 - -[Contents:] - -Some potentials that are also implemented in the Yet Another Force Field ("YAFF"_yaff) code. -The expressions and their use are discussed in the following papers - -Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) "link"_vanduyfhuys2015 -Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) "link"_vanduyfhuys2018 :ul - -which discuss the "QuickFF"_quickff methodology. - - -:link(vanduyfhuys2015,http://dx.doi.org/10.1002/jcc.23877) -:link(vanduyfhuys2018,http://dx.doi.org/10.1002/jcc.25173) -:link(quickff,http://molmod.github.io/QuickFF) -:link(yaff,https://github.com/molmod/yaff) - - -[Author:] Steven Vandenbrande. - -[Supporting info:] - -src/USER-YAFF/README -"angle_style cross"_angle_cross.html -"angle_style mm3"_angle_mm3.html -"bond_style mm3"_bond_mm3.html -"improper_style distharm"_improper_distharm.html -"improper_style sqdistharm"_improper_sqdistharm.html -"pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html -"pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html -examples/USER/yaff :ul diff --git a/doc/txt/fix.txt b/doc/txt/fix.txt deleted file mode 100644 index fd281bce83..0000000000 --- a/doc/txt/fix.txt +++ /dev/null @@ -1,392 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -fix command :h3 - -[Syntax:] - -fix ID group-ID style args :pre - -ID = user-assigned name for the fix -group-ID = ID of the group of atoms to apply the fix to -style = one of a long list of possible style names (see below) -args = arguments used by a particular style :ul - -[Examples:] - -fix 1 all nve -fix 3 all nvt temp 300.0 300.0 0.01 -fix mine top setforce 0.0 NULL 0.0 :pre - -[Description:] - -Set a fix that will be applied to a group of atoms. In LAMMPS, a -"fix" is any operation that is applied to the system during -timestepping or minimization. Examples include updating of atom -positions and velocities due to time integration, controlling -temperature, applying constraint forces to atoms, enforcing boundary -conditions, computing diagnostics, etc. There are hundreds of fixes -defined in LAMMPS and new ones can be added; see the -"Modify"_Modify.html doc page for details. - -Fixes perform their operations at different stages of the timestep. -If 2 or more fixes operate at the same stage of the timestep, they are -invoked in the order they were specified in the input script. - -The ID of a fix can only contain alphanumeric characters and -underscores. - -Fixes can be deleted with the "unfix"_unfix.html command. - -NOTE: The "unfix"_unfix.html command is the only way to turn off a -fix; simply specifying a new fix with a similar style will not turn -off the first one. This is especially important to realize for -integration fixes. For example, using a "fix nve"_fix_nve.html -command for a second run after using a "fix nvt"_fix_nh.html command -for the first run, will not cancel out the NVT time integration -invoked by the "fix nvt" command. Thus two time integrators would be -in place! - -If you specify a new fix with the same ID and style as an existing -fix, the old fix is deleted and the new one is created (presumably -with new settings). This is the same as if an "unfix" command were -first performed on the old fix, except that the new fix is kept in the -same order relative to the existing fixes as the old one originally -was. Note that this operation also wipes out any additional changes -made to the old fix via the "fix_modify"_fix_modify.html command. - -The "fix modify"_fix_modify.html command allows settings for some -fixes to be reset. See the doc page for individual fixes for details. - -Some fixes store an internal "state" which is written to binary -restart files via the "restart"_restart.html or -"write_restart"_write_restart.html commands. This allows the fix to -continue on with its calculations in a restarted simulation. See the -"read_restart"_read_restart.html command for info on how to re-specify -a fix in an input script that reads a restart file. See the doc pages -for individual fixes for info on which ones can be restarted. - -:line - -Some fixes calculate one of three styles of quantities: global, -per-atom, or local, which can be used by other commands or output as -described below. A global quantity is one or more system-wide values, -e.g. the energy of a wall interacting with particles. A per-atom -quantity is one or more values per atom, e.g. the displacement vector -for each atom since time 0. Per-atom values are set to 0.0 for atoms -not in the specified fix group. Local quantities are calculated by -each processor based on the atoms it owns, but there may be zero or -more per atoms. - -Note that a single fix can produce either global or per-atom or local -quantities (or none at all), but not both global and per-atom. It can -produce local quantities in tandem with global or per-atom quantities. -The fix doc page will explain. - -Global, per-atom, and local quantities each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for each fix describes the style and kind of values it -produces, e.g. a per-atom vector. Some fixes produce more than one -kind of a single style, e.g. a global scalar and a global vector. - -When a fix quantity is accessed, as in many of the output commands -discussed below, it can be referenced via the following bracket -notation, where ID is the ID of the fix: - -f_ID | entire scalar, vector, or array -f_ID\[I\] | one element of vector, one column of array -f_ID\[I\]\[J\] | one element of array :tb(s=|) - -In other words, using one bracket reduces the dimension of the -quantity once (vector -> scalar, array -> vector). Using two brackets -reduces the dimension twice (array -> scalar). Thus a command that -uses scalar fix values as input can also process elements of a vector -or array. - -Note that commands and "variables"_variable.html which use fix -quantities typically do not allow for all kinds, e.g. a command may -require a vector of values, not a scalar. This means there is no -ambiguity about referring to a fix quantity as f_ID even if it -produces, for example, both a scalar and vector. The doc pages for -various commands explain the details. - -:line - -In LAMMPS, the values generated by a fix can be used in several ways: - -Global values can be output via the "thermo_style -custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command. -Or the values can be referenced in a "variable equal"_variable.html or -"variable atom"_variable.html command. :ulb,l - -Per-atom values can be output via the "dump custom"_dump.html command. -Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html -command or reduced by the "compute reduce"_compute_reduce.html -command. Or the per-atom values can be referenced in an "atom-style -variable"_variable.html. :l - -Local values can be reduced by the "compute -reduce"_compute_reduce.html command, or histogrammed by the "fix -ave/histo"_fix_ave_histo.html command. :l -:ule - -See the "Howto output"_Howto_output.html doc page for a summary of -various LAMMPS output options, many of which involve fixes. - -The results of fixes that calculate global quantities can be either -"intensive" or "extensive" values. Intensive means the value is -independent of the number of atoms in the simulation, -e.g. temperature. Extensive means the value scales with the number of -atoms in the simulation, e.g. total rotational kinetic energy. -"Thermodynamic output"_thermo_style.html will normalize extensive -values by the number of atoms in the system, depending on the -"thermo_modify norm" setting. It will not normalize intensive values. -If a fix value is accessed in another way, e.g. by a -"variable"_variable.html, you may want to know whether it is an -intensive or extensive value. See the doc page for individual fixes -for further info. - -:line - -Each fix style has its own doc page which describes its arguments and -what it does, as listed below. Here is an alphabetic list of fix -styles available in LAMMPS. They are also listed in more compact form -on the "Commands fix"_Commands_fix.html doc page. - -There are also additional accelerated fix styles included in the -LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. -The individual style names on the "Commands fix"_Commands_fix.html doc -page are followed by one or more of (g,i,k,o,t) to indicate which -accelerated styles exist. - -"adapt"_fix_adapt.html - change a simulation parameter over time -"adapt/fep"_fix_adapt_fep.html - enhanced version of fix adapt -"addforce"_fix_addforce.html - add a force to each atom -"addtorque"_fix_addtorque.html - add a torque to a group of atoms -"append/atoms"_fix_append_atoms.html - append atoms to a running simulation -"atc"_fix_atc.html - initiates a coupled MD/FE simulation -"atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping -"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities -"ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities -"ave/correlate"_fix_ave_correlate.html - compute/output time correlations -"ave/correlate/long"_fix_ave_correlate_long.html - -"ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms -"ave/histo/weight"_fix_ave_histo.html - weighted version of fix ave/histo -"ave/time"_fix_ave_time.html - compute/output global time-averaged quantities -"aveforce"_fix_aveforce.html - add an averaged force to each atom -"balance"_fix_balance.html - perform dynamic load-balancing -"bocs"_fix_bocs.html - NPT style time integration with pressure correction -"bond/break"_fix_bond_break.html - break bonds on the fly -"bond/create"_fix_bond_create.html - create bonds on the fly -"bond/react"_fix_bond_react.html - apply topology changes to model reactions -"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping -"box/relax"_fix_box_relax.html - relax box size during energy minimization -"client/md"_fix_client_md.html - MD client for client/server simulations -"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field -"colvars"_fix_colvars.html - interface to the collective variables "Colvars" library -"controller"_fix_controller.html - apply control loop feedback mechanism -"deform"_fix_deform.html - change the simulation box size/shape -"deposit"_fix_deposit.html - add new atoms above a surface -"dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics -"drag"_fix_drag.html - drag atoms towards a defined coordinate -"drude"_fix_drude.html - part of Drude oscillator polarization model -"drude/transform/direct"_fix_drude_transform.html - part of Drude oscillator polarization model -"drude/transform/inverse"_fix_drude_transform.html - part of Drude oscillator polarization model -"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces -"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations -"efield"_fix_efield.html - impose electric field on system -"ehex"_fix_ehex.html - enhanced heat exchange algorithm -"electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force -"enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force -"eos/cv"_fix_eos_cv.html - -"eos/table"_fix_eos_table.html - -"eos/table/rx"_fix_eos_table_rx.html - -"evaporate"_fix_evaporate.html - remove atoms from simulation periodically -"external"_fix_external.html - callback to an external driver program -"ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat -"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA -"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux -"freeze"_fix_freeze.html - freeze atoms in a granular simulation -"gcmc"_fix_gcmc.html - grand canonical insertions/deletions -"gld"_fix_gld.html - generalized Langevin dynamics integrator -"gle"_fix_gle.html - generalized Langevin equation thermostat -"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation -"grem"_fix_grem.html - implements the generalized replica exchange method -"halt"_fix_halt.html - terminate a dynamics run or minimization -"heat"_fix_heat.html - add/subtract momentum-conserving heat -"hyper/global"_fix_hyper_global.html - global hyperdynamics -"hyper/local"_fix_hyper_local.html - local hyperdynamics -"imd"_fix_imd.html - implements the "Interactive MD" (IMD) protocol -"indent"_fix_indent.html - impose force due to an indenter -"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations -"langevin"_fix_langevin.html - Langevin temperature control -"langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators -"langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model -"langevin/spin"_fix_langevin_spin.html - Langevin temperature control for a spin or spin-lattice system -"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code -"lb/fluid"_fix_lb_fluid.html - -"lb/momentum"_fix_lb_momentum.html - -"lb/pc"_fix_lb_pc.html - -"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html - -"lb/viscous"_fix_lb_viscous.html - -"lineforce"_fix_lineforce.html - constrain atoms to move in a line -"manifoldforce"_fix_manifoldforce.html - restrain atoms to a manifold during minimization -"meso"_fix_meso.html - time integration for SPH/DPDE particles -"meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion -"meso/stationary"_fix_meso_stationary.html - -"momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms -"move"_fix_move.html - move atoms in a prescribed fashion -"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models -"msst"_fix_msst.html - multi-scale shock technique (MSST) integration -"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm -"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm -"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm -"neb"_fix_neb.html - nudged elastic band (NEB) spring forces -"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover -"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles -"nph/body"_fix_nph_body.html - NPH for body particles -"nph/eff"_fix_nh_eff.html - NPH for nuclei and electrons in the electron force field model -"nph/sphere"_fix_nph_sphere.html - NPH for spherical particles -"nphug"_fix_nphug.html - constant-stress Hugoniostat integration -"npt"_fix_nh.html - constant NPT time integration via Nose/Hoover -"npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles -"npt/body"_fix_npt_body.html - NPT for body particles -"npt/eff"_fix_nh_eff.html - NPT for nuclei and electrons in the electron force field model -"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles -"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow -"nve"_fix_nve.html - constant NVE time integration -"nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles -"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces -"nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model -"nve/body"_fix_nve_body.html - NVE for body particles -"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models -"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models -"nve/eff"_fix_nve_eff.html - NVE for nuclei and electrons in the electron force field model -"nve/limit"_fix_nve_limit.html - NVE with limited step length -"nve/line"_fix_nve_line.html - NVE for line segments -"nve/manifold/rattle"_fix_nve_manifold_rattle.html - -"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only) -"nve/sphere"_fix_nve_sphere.html - NVE for spherical particles -"nve/spin"_fix_nve_spin.html - NVE for a spin or spin-lattice system -"nve/tri"_fix_nve_tri.html - NVE for triangles -"nvk"_fix_nvk.html - constant kinetic energy time integration -"nvt"_fix_nh.html - NVT time integration via Nose/Hoover -"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles -"nvt/body"_fix_nvt_body.html - NVT for body particles -"nvt/eff"_fix_nh_eff.html - NVE for nuclei and electrons in the electron force field model -"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html - -"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations -"nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model -"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles -"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow -"oneway"_fix_oneway.html - constrain particles on move in one direction -"orient/bcc"_fix_orient.html - add grain boundary migration force for BCC -"orient/fcc"_fix_orient.html - add grain boundary migration force for FCC -"phonon"_fix_phonon.html - calculate dynamical matrix from MD simulations -"pimd"_fix_pimd.html - Feynman path integral molecular dynamics -"planeforce"_fix_planeforce.html - constrain atoms to move in a plane -"plumed"_fix_plumed.html - wrapper on PLUMED free energy library -"poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies -"pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain -"precession/spin"_fix_precession_spin.html - -"press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat -"print"_fix_print.html - print text and variables during a simulation -"property/atom"_fix_property_atom.html - add customized per-atom values -"python/invoke"_fix_python_invoke.html - call a Python function during a simulation -"python/move"_fix_python_move.html - call a Python function during a simulation run -"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator -"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential -"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method -"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer -"qeq/point"_fix_qeq.html - charge equilibration via point method -"qeq/reax"_fix_qeq_reax.html - charge equilibration for ReaxFF potential -"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method -"qeq/slater"_fix_qeq.html - charge equilibration via Slater method -"qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling -"qtb"_fix_qtb.html - implement quantum thermal bath scheme -"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles -"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information -"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information -"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms -"restrain"_fix_restrain.html - constrain a bond, angle, dihedral -"rhok"_fix_rhok.html - add bias potential for long-range ordered systems -"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration -"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body -"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration -"rigid/nph/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration -"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration -"rigid/npt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration -"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration -"rigid/nve/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration -"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration -"rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration -"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration -"rx"_fix_rx.html - -"saed/vtk"_fix_saed_vtk.html - -"setforce"_fix_setforce.html - set the force on each atom -"shake"_fix_shake.html - SHAKE constraints on bonds and/or angles -"shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting -"smd"_fix_smd.html - applied a steered MD force to a group -"smd/adjust_dt"_fix_smd_adjust_dt.html - -"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html - -"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html - -"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html - -"smd/setvel"_fix_smd_setvel.html - -"smd/wall_surface"_fix_smd_wall_surface.html - -"spring"_fix_spring.html - apply harmonic spring force to group of atoms -"spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms -"spring/rg"_fix_spring_rg.html - spring on radius of gyration of group of atoms -"spring/self"_fix_spring_self.html - spring from each atom to its origin -"srd"_fix_srd.html - stochastic rotation dynamics (SRD) -"store/force"_fix_store_force.html - store force on each atom -"store/state"_fix_store_state.html - store attributes for each atom -"tdpd/source"_fix_dpd_source.html - -"temp/berendsen"_fix_temp_berendsen.html - temperature control by Berendsen thermostat -"temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics -"temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics -"temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling -"temp/rescale/eff"_fix_temp_rescale_eff.html - temperature control by velocity rescaling in the electron force field model -"tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method -"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation -"ti/spring"_fix_ti_spring.html - -"tmd"_fix_tmd.html - guide a group of atoms to a new configuration -"ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling -"ttm/mod"_fix_ttm.html - enhanced two-temperature model with additional options -"tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters -"vector"_fix_vector.html - accumulate a global vector every N timesteps -"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation -"viscous"_fix_viscous.html - viscous damping for granular simulations -"wall/body/polygon"_fix_wall_body_polygon.html - -"wall/body/polyhedron"_fix_wall_body_polyhedron.html - -"wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles -"wall/ees"_fix_wall_ees.html - wall for ellipsoidal particles -"wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations -"wall/gran/region"_fix_wall_gran_region.html - -"wall/harmonic"_fix_wall.html - harmonic spring wall -"wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall -"wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall -"wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall -"wall/morse"_fix_wall.html - Morse potential wall -"wall/piston"_fix_wall_piston.html - moving reflective piston wall -"wall/reflect"_fix_wall_reflect.html - reflecting wall(s) -"wall/region"_fix_wall_region.html - use region surface as wall -"wall/region/ees"_fix_wall_ees.html - use region surface as wall for ellipsoidal particles -"wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul - -[Restrictions:] - -Some fix styles are part of specific packages. They are only enabled -if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. The doc pages for -individual fixes tell if it is part of a package. - -[Related commands:] - -"unfix"_unfix.html, "fix_modify"_fix_modify.html - -[Default:] none